Now mmCIF files that have no author fields in atom_site can be read (e.g. from PyMol or ESMAtlas) #775 #1083
No evaluations of arguments in debug level log statements #1086 #789
Removed
Minor removal from biojava-core: FileDownloadUtils::copy, replaced by Files::copy
biojava-7.1.0
2 months ago
Added
Class FastaStreamer to read FASTA-formatted files using Java streams
Fixed
Various minor fixes for code smells
Some dependency upgrades
Now using Jakarta as the JAXB implementation #1076
Fixed SCOP URL #1077
biojava-7.0.2
11 months ago
Added
Some more categories related to entity are now written in mmCIF writer #1063
Fixed
Not declaring anymore unchecked exceptions in signatures #1062
biojava-7.0.1
1 year ago
Fixed
The jar packages now contain pom.properties files #1057
Some minor improvements in a few biojava-structure methods #1058
biojava-7.0.0
1 year ago
Breaking
BioJava is now compiled at JDK 11 compatibility level. It will not work anymore under older JREs (e.g. JRE 8).
This is the main reason for the major version bump.
Added
Better handling of downloads: file download validation #1024
Fixed
Upgrade to latest ciftools-java, fixes non-US locale issue #1049
Issue with some edge cases in CIF parsing #1054
Minor security issue #1046
biojava-6.1.0
1 year ago
Added
GenBankWriterHelper - method that uses the original locus line rather than creating a new one, preventing loss of information
GenBankReader - the ability to successfully parse GenBank files with a LOCUS ID containing white space
GenBankReader - the ability to successfully parse GenBank files missing a LOCUS ID
Aromaticity calculation in biojava-aa-prop module
Fixed
GenBankWriter - String Formatter error when key or value of Qualifier has character "%", #886
GenBankWriter - outputting the accession version and GI ID
GenBankWriter - outputting feature locations containing joins and partial locations
GenBankReader - reading locations split over multiple lines
GenBankReader - set if feature qualifier values require quotes
Local alignment with linear gap penalty was producing an NPE, #1036
New default server for PDB files. Note that from Aug 2023 older versions of BioJava will not be able to fetch PDB files unless PDB.FILE.SERVER system property is used to override the default server
Dependency upgrades
Some bug and security fixes
biojava-6.0.5
2 years ago
Fixed
Null handling in a few places related to loading PDB, CIF, mmtf files (issue introduced in 6.0.0). #1019
biojava-6.0.4
2 years ago
Fixed
Log4j dependency upgraded to 2.17.1 to avoid new vulnerabilities
Some new tests
Fixes in tests and docs
Bugfix in LocalProteinDomainParser #1009
biojava-6.0.3
2 years ago
Fixed
Log4j dependency upgraded to 2.16.0, to avoid log4hshell vulnerability
biojava-6.0.2
2 years ago
Fixed
Log4j dependency upgraded to 2.15.0, to avoid log4hshell vulnerability